{
  "_id": "6a1aed321d7bb097a09f4d63",
  "Package": "qPLEXanalyzer",
  "Type": "Package",
  "Title": "Tools for quantitative proteomics data analysis",
  "Version": "1.31.0",
  "Date": "2026-01-28",
  "Authors@R": "c(person(\"Matthew\",\"Eldridge\", role = \"aut\"),\nperson(\"Kamal\", \"Kishore\", role = \"aut\",\nemail = \"kamal.fartiyal84@gmail.com\"),\nperson(\"Ashley\", \"Sawle\", role=c(\"aut\", \"cre\"),\nemail=\"ads2202cu@gmail.com\"))",
  "Description": "Tools for TMT based quantitative proteomics data analysis.",
  "License": "GPL-2",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, Proteomics, MassSpectrometry, Normalization,\nPreprocessing, QualityControl, DataImport",
  "BugReports": "https://github.com/crukci-bioinformatics/qPLEXanalyzer/issues",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev libx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:15 UTC",
  "RemoteUrl": "https://github.com/bioc/qPLEXanalyzer",
  "RemoteRef": "HEAD",
  "RemoteSha": "cc7b6461160740f6f2723cb236588688d2a01444",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:40:12 UTC",
    "User": "root"
  },
  "Author": "Matthew Eldridge [aut],\nKamal Kishore [aut],\nAshley Sawle [aut, cre]",
  "Maintainer": "Ashley Sawle <ads2202cu@gmail.com>",
  "MD5sum": "51d2c20e80f3e8c206c929a74cfb4617",
  "_user": "bioc",
  "_type": "src",
  "_file": "qPLEXanalyzer_1.31.0.tar.gz",
  "_fileid": "5b17e27e77f6637972b9696a9662e96da213944edcd2c254cc168775cec34174",
  "_filesize": 4888748,
  "_sha256": "5b17e27e77f6637972b9696a9662e96da213944edcd2c254cc168775cec34174",
  "_created": "2026-05-30T09:40:12.000Z",
  "_published": "2026-05-30T13:59:14.505Z",
  "_jobs": [
    {
      "job": 78640293840,
      "time": 235,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307388029"
    },
    {
      "job": 78640293821,
      "time": 455,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307407125"
    },
    {
      "job": 78640293831,
      "time": 465,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307407978"
    },
    {
      "job": 78640293827,
      "time": 254,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308689896"
    },
    {
      "job": 78640293834,
      "time": 284,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7308693270"
    },
    {
      "job": 78639580183,
      "time": 344,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307251193"
    },
    {
      "job": 78640293829,
      "time": 176,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307382602"
    },
    {
      "job": 78640293835,
      "time": 332,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307396753"
    },
    {
      "job": 78640293839,
      "time": 314,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307395179"
    },
    {
      "job": 78640293833,
      "time": 322,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307395858"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/qPLEXanalyzer",
  "_commit": {
    "id": "cc7b6461160740f6f2723cb236588688d2a01444",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380495
  },
  "_maintainer": {
    "name": "Ashley Sawle",
    "email": "ads2202cu@gmail.com",
    "login": "ashkernow",
    "description": "",
    "uuid": 6537640
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "MSnbase",
      "role": "Depends"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "ggdendro",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "MSnbase",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "MSnbase",
      "role": "Suggests"
    },
    {
      "package": "qPLEXdata",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "statmod",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "UniProt.ws",
      "role": "Suggests"
    },
    {
      "package": "vdiffr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-03",
      "n": 4
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-05",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "proteomics",
    "massspectrometry",
    "normalization",
    "preprocessing",
    "qualitycontrol",
    "dataimport"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "ashkernow",
      "count": 327,
      "uuid": 6537640
    },
    {
      "user": "kamalfartiyal84",
      "count": 81,
      "uuid": 14331074
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 400,
    "source": "https://www.bioconductor.org/packages/stats/bioc/qPLEXanalyzer"
  },
  "_mentions": 6,
  "_devurl": "https://github.com/crukci-bioinformatics/qplexanalyzer",
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/qPLEXanalyzer.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/crukci-bioinformatics/qplexanalyzer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "assignColours",
    "coefVar",
    "computeDiffStats",
    "convertToMSnset",
    "corrPlot",
    "coveragePlot",
    "getContrastResults",
    "groupScaling",
    "hierarchicalPlot",
    "intensityBoxplot",
    "intensityPlot",
    "IRSnorm",
    "maVolPlot",
    "mergePeptides",
    "mergeSites",
    "normalizeQuantiles",
    "normalizeScaling",
    "pcaPlot",
    "peptideIntensityPlot",
    "plotMeanVar",
    "regressIntensity",
    "rliPlot",
    "rowScaling",
    "summarizeIntensities"
  ],
  "_datasets": [
    {
      "name": "ER_ARID1A_KO_MCF7",
      "title": "ER_ARID1A_KO_MCF7 dataset",
      "object": "ER_ARID1A_KO_MCF7",
      "file": "ER_ARID1A_KO_MCF7.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "exp2_Xlink",
      "title": "exp2_Xlink dataset",
      "object": "exp2_Xlink",
      "file": "exp2_Xlink.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "exp3_OHT_ESR1",
      "title": "exp3_OHT_ESR1 dataset",
      "object": "exp3_OHT_ESR1",
      "file": "exp3_OHT_ESR1.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "human_anno",
      "title": "human_anno dataset",
      "object": "human_anno",
      "file": "human_anno.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Accessions",
        "Gene",
        "Description",
        "GeneSymbol"
      ],
      "rows": 20386,
      "table": true,
      "tojson": true
    },
    {
      "name": "mouse_anno",
      "title": "mouse_anno dataset",
      "object": "mouse_anno",
      "file": "mouse_anno.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Accessions",
        "Gene",
        "Description",
        "GeneSymbol"
      ],
      "rows": 17119,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "qPLEXanalyzer-package",
      "title": "Tools for qPLEX-RIME data analysis",
      "topics": [
        "qPLEXanalyzer-package",
        "qPLEXanalyzer"
      ]
    },
    {
      "page": "assignColours",
      "title": "Assigns colours to samples in groups",
      "topics": [
        "assignColours"
      ]
    },
    {
      "page": "coefVar",
      "title": "Calculating the coefficient of variation by utilizing expression data within individual sample groups.",
      "topics": [
        "coefVar"
      ]
    },
    {
      "page": "computeDiffStats",
      "title": "Compute differential statistics",
      "topics": [
        "computeDiffStats"
      ]
    },
    {
      "page": "convertToMSnset",
      "title": "Converts proteomics TMT intensity data to MSnSet",
      "topics": [
        "convertToMSnset"
      ]
    },
    {
      "page": "corrPlot",
      "title": "Correlation plot",
      "topics": [
        "corrPlot"
      ]
    },
    {
      "page": "coveragePlot",
      "title": "Plot peptide sequence coverage",
      "topics": [
        "coveragePlot"
      ]
    },
    {
      "page": "ER_ARID1A_KO_MCF7",
      "title": "ER_ARID1A_KO_MCF7 dataset",
      "topics": [
        "ER_ARID1A_KO_MCF7"
      ]
    },
    {
      "page": "exp2_Xlink",
      "title": "exp2_Xlink dataset",
      "topics": [
        "exp2_Xlink"
      ]
    },
    {
      "page": "exp3_OHT_ESR1",
      "title": "exp3_OHT_ESR1 dataset",
      "topics": [
        "exp3_OHT_ESR1"
      ]
    },
    {
      "page": "getContrastResults",
      "title": "Get differential statistics results",
      "topics": [
        "getContrastResults"
      ]
    },
    {
      "page": "groupScaling",
      "title": "Normalization by scaling within group",
      "topics": [
        "groupScaling"
      ]
    },
    {
      "page": "hierarchicalPlot",
      "title": "Hierarchical clustering plot",
      "topics": [
        "hierarchicalPlot"
      ]
    },
    {
      "page": "human_anno",
      "title": "human_anno dataset",
      "topics": [
        "human_anno"
      ]
    },
    {
      "page": "intensityBoxplot",
      "title": "Intensity Distribution boxplot",
      "topics": [
        "intensityBoxplot"
      ]
    },
    {
      "page": "intensityPlot",
      "title": "Intensity Distribution Plot",
      "topics": [
        "intensityPlot"
      ]
    },
    {
      "page": "IRSnorm",
      "title": "Batch Correction by Internal Reference Scale",
      "topics": [
        "IRSnorm"
      ]
    },
    {
      "page": "maVolPlot",
      "title": "MA or Volcano Plot",
      "topics": [
        "maVolPlot"
      ]
    },
    {
      "page": "mergePeptides",
      "title": "Merge identical modified peptides intensities",
      "topics": [
        "mergePeptides"
      ]
    },
    {
      "page": "mergeSites",
      "title": "Merge identical modification sites intensities",
      "topics": [
        "mergeSites"
      ]
    },
    {
      "page": "mouse_anno",
      "title": "mouse_anno dataset",
      "topics": [
        "mouse_anno"
      ]
    },
    {
      "page": "normalizeQuantiles",
      "title": "Quantile normalization",
      "topics": [
        "normalizeQuantiles"
      ]
    },
    {
      "page": "normalizeScaling",
      "title": "Normalization by scaling",
      "topics": [
        "normalizeScaling"
      ]
    },
    {
      "page": "pcaPlot",
      "title": "PCA plot",
      "topics": [
        "pcaPlot"
      ]
    },
    {
      "page": "peptideIntensityPlot",
      "title": "Plot peptide intensities",
      "topics": [
        "peptideIntensityPlot"
      ]
    },
    {
      "page": "plotMeanVar",
      "title": "Mean variance plot",
      "topics": [
        "plotMeanVar"
      ]
    },
    {
      "page": "regressIntensity",
      "title": "Regression based analysis",
      "topics": [
        "regressIntensity"
      ]
    },
    {
      "page": "rliPlot",
      "title": "Relative log intensity plot",
      "topics": [
        "rliPlot"
      ]
    },
    {
      "page": "rowScaling",
      "title": "Normalization by scaling peptide/protein intensity across all samples",
      "topics": [
        "rowScaling"
      ]
    },
    {
      "page": "summarizeIntensities",
      "title": "Summarizes peptides intensities to proteins",
      "topics": [
        "summarizeIntensities"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "AnnotationFilter",
    "askpass",
    "assertthat",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bslib",
    "cachem",
    "cli",
    "clipr",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggdendro",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "magrittr",
    "MALDIquant",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "MsCoreUtils",
    "MSnbase",
    "MultiAssayExperiment",
    "mzID",
    "mzR",
    "ncdf4",
    "openssl",
    "otel",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "preprocessCore",
    "prettyunits",
    "progress",
    "promises",
    "ProtGenerics",
    "PSMatch",
    "PTMods",
    "purrr",
    "QFeatures",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "reshape2",
    "Rhdf5lib",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "Spectra",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "vsn",
    "withr",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "qPLEXanalyzer.Rmd",
      "filename": "qPLEXanalyzer.html",
      "title": "qPLEXanalyzer",
      "author": "Matthew Eldridge, Kamal Kishore and Ashley Sawle",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Import quantitative dataset",
        "Quality control",
        "Peptide intensity plots",
        "Relative log intensity boxplot",
        "Sample correlation plot",
        "Hierachical clustering dendrogram",
        "Principle component analysis scatterplot",
        "Bait protein coverage plot",
        "Data normalization",
        "Aggregation of peptide intensities into protein intensities",
        "Merging of similar peptides/sites into unified intensities",
        "Regression Analysis",
        "Differential statistical analysis",
        "Session Information"
      ],
      "created": "2020-09-18 14:39:05",
      "modified": "2026-01-14 11:23:19",
      "commits": 6
    }
  ],
  "_score": 5.079181246047625,
  "_indexed": true,
  "_nocasepkg": "qplexanalyzer",
  "_universes": [
    "bioc",
    "ashkernow",
    "crukci-bioinformatics"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T10:04:16.000Z",
      "distro": "noble",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "3db95b41d1bed31125eb4f38f693725aee89ca78ad1d1084d02470a6fb41ba8b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T10:04:22.000Z",
      "distro": "noble",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "905db5d4e5b562f4f48d2165912db5a8b61d8c324b0ebc860556eda65cf23a4a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T13:55:26.000Z",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "b2faf60ed5ec16e445ed82d5397a444b079d9ac43644abce9d9c9329a847c313",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T13:55:49.000Z",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "f44106a1dd9e94f142db707146938de5ba57bb1118a2ad510e12ee662ebdf73e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-05-30T10:03:27.000Z",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "59416aa593d9d17dcee228ec4a158ac0362c3fafdf20951d398f1ede38df0aa3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T10:02:18.000Z",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "ce4d1f073587e22f8a16c8eeddcafd91405570bb7aad79e75f9bd71f56554e9b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T10:02:07.000Z",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "f25893fc621bc85050168404e0c636c9c0f9536014410b3828ecb8817652d71d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T10:02:04.000Z",
      "commit": "cc7b6461160740f6f2723cb236588688d2a01444",
      "fileid": "d755c9b1b59fcaa0b1dc4cbf10c4bfc9864dc07684f7d18046f0b7a4d5ecbe85",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676241112"
    }
  ]
}